as.data.frame.crm_fit   Convert crm_fit object to 'data.frame'.
as.data.frame.efftox_fit
                        Convert efftox_fit object to 'data.frame'.
as.mcmc.list.crm_fit    Convert 'crm_fit' to instance of 'mcmc.list'
as.mcmc.list.efftox_fit
                        Convert 'efftox_fit' to instance of 'mcmc.list'
as_tibble.augbin_2t_1a_fit
                        Cast 'augbin_2t_1a_fit' object to 'tibble'.
as_tibble.dose_finding_paths
                        Cast 'dose_finding_paths' object to 'tibble'.
augbin_2t_1a_fit        Class used by 'trialr' to fit Wason & Seaman's
                        Augmented Binary method in single arm trials
                        with two post-baseline tumour assessments.
augbin_fit              Class used by 'trialr' to fit Wason & Seaman's
                        Augmented Binary method.
binary_prob_success     Calculate the binary probability of success.
careful_escalation      Dose selection function that practices careful
                        escalation.
closest_to_target       Get index of element in vector with value
                        closest to a target
crm_codified_dose_logistic
                        Calculate codified CRM doses.
crm_dtps                Calculate dose-transition pathways for a CRM
                        study
crm_fit-class           Class of model fit by 'trialr' using the CRM
                        dose-finding design.
crm_params-class        Container class for parameters to fit the CRM
                        models in trialr.
crm_path_analysis       Fit a CRM model to the incrementally observed
                        outcomes on a trial pathway.
crm_prior_beliefs       Get the prior beliefs for a CRM trial scenario.
crm_process             Process RStan samples from a CRM model.
df_parse_outcomes       Parse a string of dose-finding trial outcomes
                        to binary vector notation.
dose_finding_fit-class
                        Class of dose-finding model fit by 'trialr'
                        using Stan.
dose_finding_path_node-class
                        Class to hold the elements of a single
                        dose-finding analysis residing in a pathway of
                        analyses.
eff_at_dose             Get the number of efficacy events seen at the
                        doses under investigation.
efftox_analysis_to_df   EffTox analysis to data.frame
efftox_contour_plot     Plot EffTox utility contours
efftox_dtps             Calculate dose-transition pathways for an
                        EffTox study
efftox_dtps_to_dataframe
                        Calculate dose-transition pathways for an
                        EffTox study
efftox_fit-class        Class of model fit by 'trialr' using the EffTox
                        dose-finding design.
efftox_get_tox          Get the Prob(Tox) for Prob(Eff) and utility
                        pairs
efftox_parameters_demo
                        Get parameters to run the EffTox demo
efftox_params-class     Container class for parameters to fit the
                        EffTox model in trialr.
efftox_parse_outcomes   Parse a string of EffTox outcomes to binary
                        vector notation.
efftox_path_analysis    Fit an EffTox model to the incrementally
                        observed outcomes on a trial pathway.
efftox_process          Process RStan samples from an EffTox model
efftox_simulate         Run EffTox simulations
efftox_solve_p          Calculate the p-index for EffTox utility
                        contours
efftox_superiority      Get dose-superiority matrix in EffTox
efftox_utility          Get the utility of efficacy & toxicity
                        probability pairs
efftox_utility_density_plot
                        Plot densities of EffTox dose utilities
n_at_dose               Get the number of patients treated at the doses
                        under investigation.
parse_dose_finding_outcomes
                        Parse a string of dose-finding trial outcomes.
parse_eff_tox_dose_finding_outcomes
                        Parse a string of phase I/II dose-finding trial
                        outcomes.
peps2_get_data          Get data to run the PePS2 trial example
peps2_process           Process RStan samples from a BEBOP model fit to
                        PePS2 data
plot.crm_fit            Plot an crm_fit
plot.efftox_fit         Plot an efftox_fit
predict.augbin_2t_1a_fit
                        Predict probability of success for given tumour
                        size measurements.
print.augbin_fit        Print augbin_fit object.
print.crm_fit           Print crm_fit object.
print.efftox_fit        Print efftox_fit object.
prior_predictive_augbin_2t_1a
                        Sample data from the Augmented Binary model
                        prior predictive distribution.
prob_success            Calculate the probability of success.
prob_tox_exceeds        Calculate the probability that the rate of
                        toxicity exceeds some threshold
ranBin2                 Sample pairs of correlated binary events
rlkjcorr                Sample LKJ correlation matrices.
spread_paths            Spread the information in dose_finding_paths
                        object to a wide data.frame format.
stan_augbin             Fit Wason & Seaman's Augmented Binary model for
                        tumour response.
stan_augbin_demo        Simple helper function to demonstrate fitting
                        of an Augmented Binary model.
stan_crm                Fit a CRM model
stan_efftox             Fit an EffTox model
stan_efftox_demo        Fit the EffTox model presented in Thall et al.
                        (2014)
stan_hierarchical_response_thall
                        Fit the hierarchical response model described
                        by Thall _et al._ (2003).
stan_peps2              Fit the P2TNE model developed for the PePS2
                        trial to some outcomes.
summary.crm_fit         Obtain summary of an crm_fit
summary.efftox_fit      Obtain summary of an efftox_fit
total_weight_at_dose    Get the total weight of patient outcomes at the
                        doses under investigation.
tox_at_dose             Get the number of toxicity events seen at the
                        doses under investigation.
trialr-package          The 'trialr' package.
trialr_simulate         Run a simulation study.
weights_at_dose         Get the weights of patient outcomes at the
                        doses under investigation.
